Thanks to Greg Folkers for sending the link to this Journal of Virology report by an team of Italian researchers: Emergence of a Highly Pathogenic Avian Influenza Virus from a Low Pathogenic Progenitor. The abstract:
Avian influenza (AI) viruses of the H7 subtype have the potential to evolve into highly pathogenic (HP) viruses that represent a major economic problem for the poultry industry and a threat to global health. However, the emergence of HPAI viruses from low pathogenic (LPAI) progenitor viruses is currently poorly understood.
To investigate the origin and evolution of one of the most important avian influenza epidemics described in Europe, we investigated the evolutionary and spatial dynamics of the entire genome of 109 H7N1 (46 LPAI and 63 HPAI) viruses collected during Italian H7N1 outbreaks between March 1999 and February 2001. Phylogenetic analysis revealed that the LPAI and HPAI epidemics shared a single ancestor, that the HPAI strains evolved from the LPAI viruses in the absence of reassortment, and that there was a parallel emergence of mutations among HPAI and later LPAI lineages.
Notably, an ultra-deep sequencing analysis demonstrated that some of the amino acid changes characterizing the HPAI virus cluster were already present with low frequency within several individual viral populations from the beginning of the LPAI H7N1 epidemic. A Bayesian phylogeographic analysis revealed stronger spatial structure during the LPAI outbreak, reflecting the more rapid spread of the virus following the emergence of HPAI.
The data generated in this study provide the most complete evolutionary and phylogeographic analysis of epidemiologically intertwined high and low pathogenic viruses undertaken to date, and highlight the importance of implementing prompt eradication measures against LPAI to prevent the appearance of viruses with fitness advantages and unpredictable pathogenic properties.
Importance The Italian H7 avian influenza (AI) epidemic of 1999-2001 was one of the most important AI outbreaks described in Europe. H7 viruses have the ability to evolve into HP (highly pathogenic) forms from LP (low pathogenic) precursors, although the mechanisms underlying this evolutionary transition are only poorly understood.
We combined epidemiological information, whole-genome sequence data and ultra-deep sequencing approaches to provide the most complete characterization of the evolution of HPAI from LPAI viruses undertaken to date. Our analysis revealed that the LPAI viruses were the direct ancestors of the HPAI strains and identified low frequency minority variants with HPAI mutations that were present in the LPAI samples. Spatial analysis provided key information for the design of effective control strategies for AI at both local and global scales.
Overall, this work highlights the importance of implementing rapid eradication measures to prevent the emergence of novel influenza viruses with severe pathogenic properties.